
                                 showalign 



Function

   Displays a multiple sequence alignment

Description

   showalign displays an aligned set of protein or a nucleic acid
   sequences in a style suitable for publication.

   The output is sent to the screen by default for the user to view, but
   it can write the results to a file.

   The output highlights various differences or similarities between each
   of the sequences and a reference sequence by setting selected types of
   matches to a reference sequence to be '.' characters.

   The reference sequence can be either the calculated consensus sequence
   (the default) or it can be one of the set of aligned sequences,
   specified by either the ordinal number of that sequence in the input
   file, or by its name.

   The output sequences can be displayed in either the input order (the
   default) or they can be sorted in order of their similarity to the
   reference sequence or sorted alphabetically by their names.

   By using the '-show' option, the displayed sequences can either be
   shown as:
     * complete (-show=All),
     * only identical matches between the sequence and the reference
       sequence, all other positions being replaced by '.' characters
       (-show=Identities)
     * non-identical matches, with identical matches being replaced by
       '.' characters, similar matches are shown in lower case
       (-show=Non-identities)
     * similar matches, with non-similar matches being replaced by '.'
       characters, similar matches are shown in lower case
       (-show=Similarities)
     * dissimilar matches, with identical or similar matches being
       replaced by '.' characters (-show=Dissimilarities)

   A small table of the way these alignments are displayed illustrates
   this.
   If we have a reference protein sequence of "III" and a sequence
   aligned to this of "ILW", then we have an identical matching residue,
   then a similar one, then a dissimilar one.
   The different methods of display would give the following:
     _________________________________________________________________

Reference       III

All             ILw
Identical       I..
Non-id          .lW
Similar         Il.
Dissimilar      ..W
     _________________________________________________________________

   Changing the similar matches to lowercase can optionally be disable by
   using the option -nosimilarcase.

   The displayed sequence can be numbered by placing a ruler with ticks
   above the sequence.

   The width of a line can be set. The width of a margin to the left of
   the sequences that shows the sequence names can be set.

   Specified regions of the sequence can be displayed in uppercase to
   highlight them.

   The output can be formatted for HTML.

   If the output is being formatted for HTML, then specified regions of
   the sequence can be displayed in any valid HTML colours.

  The consensus line

   The consensus line can be displayed in a mixture of uppercase and
   lowercase symbols.

   The uppercase consensus symbol is indicates that the consensus is
   strong and lowercase indicates that it is weak.

   The cutoff for setting the case of the consensus is set by the
   qualifier '-setcase'. If the number of residues at that position that
   match the consensus value is greater than this, then the symbol is in
   uppercase, otherwise the symbol is in lowercase. By default, the value
   of setcase is set so that if there are more than 50% of residues
   identical to the consunsus at that position, then the consensus is in
   uppercase.

   To put all of the consensus symbols into uppercase or lowercase, make
   -setcase zero or very large (try 100000 ?).

Usage

   Here is a sample session with showalign


% showalign 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Display the sequences in order of similarity to the reference sequence


% showalign -order=s 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 3

   Format for HTML and highlight some interesting regions in different
   colours:


% showalign -html -high '4-13 green 43-43 red 51-56 blue' 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 4

   No consensus line at the bottom No ruler line No numbers line Don't
   repeat the reference sequence at the bottom of the sequences Use
   sequence 1 as the reference sequence Display residues from position 10
   to 30 only


% showalign -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 5

   Show non-identities between the sequences


% showalign -show=n 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Example 6

   Show all of the sequences


% showalign -show=a 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 7

   Show identities between the sequences


% showalign -show=i 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 8

   Show similarities between the sequences


% showalign -show=s 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 9

   Show dissimilarities between the sequences


% showalign -show=d 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 10

   Use the first sequence as the reference to compare to:


% showalign -ref=1 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 11

   Show a range of sequences in uppercase, everything else in lowercase


% showalign -nocon -ref=1 -sl -upper 9-15 -nosimilarcase 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

   Example 12

   Display the sequences in alphabetic order:


% showalign -order=a 
Displays a multiple sequence alignment
Input sequence set: globins.msf
Output file [globins.showalign]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -matrix             matrix     This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -refseq             string     If you give the number in the alignment or
                                  the name of a sequence, it will be taken to
                                  be the reference sequence. The reference
                                  sequence is always show in full and is the
                                  one against which all the other sequences
                                  are compared. If this is set to 0 then the
                                  consensus sequence will be used as the
                                  reference sequence. By default the consensus
                                  sequence is used as the reference sequence.
   -[no]bottom         boolean    If this is true then the reference sequence
                                  is displayed at the bottom of the alignment
                                  as well as at the top.
   -show               menu       What to show
   -order              menu       Output order of the sequences
   -[no]similarcase    boolean    If this is set True, then when -show is set
                                  to 'Similarities' or 'Non-identities' and a
                                  residue is similar but not identical to the
                                  reference sequence residue, it will be
                                  changed to lower-case. If -show is set to
                                  'All' then non-identical, non-similar
                                  residues will be changed to lower-case. If
                                  this is False then no change to the case of
                                  the residues is made on the basis of their
                                  similarity to the reference sequence.
   -[no]consensus      boolean    If this is true then the consensus line is
                                  displayed.

   Advanced (Unprompted) qualifiers:
   -uppercase          range      Regions to put in uppercase.
                                  If this is left blank, then the sequence
                                  case is left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99
   -[no]number         boolean    If this option is true then a line giving
                                  the positions in the alignment is displayed
                                  every 10 characters above the alignment.
   -[no]ruler          boolean    If this option is true then a ruler line
                                  marking every 5th and 10th character in the
                                  alignment is displayed.
   -width              integer    Width of sequence to display
   -margin             integer    This sets the length of the left-hand margin
                                  for sequence names. If the margin is set at
                                  0 then no margin and no names are
                                  displayed. If the margin is set to a value
                                  that is less than the length of a sequence
                                  name then the sequence name is displayed
                                  truncated to the length of the margin. If
                                  the margin is set to -1 then the minimum
                                  margin width that will allow all the
                                  sequence names to be displayed in full plus
                                  a space at the end of the name will
                                  automatically be selected.
   -html               boolean    Use HTML formatting
   -highlight          range      Regions to colour if formatting for HTML.
                                  If this is left blank, then the sequence is
                                  left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are followed by any valid HTML font
                                  colour.
                                  Examples of region specifications are:
                                  24-45 blue 56-78 orange
                                  1-100 green 120-156 red
                                  A file of ranges to colour (one range per
                                  line) can be specified as '@filename'.
   -plurality          float      Set a cut-off for the % of positive scoring
                                  matches below which there is no consensus.
                                  The default plurality is taken as 50% of the
                                  total weight of all the sequences in the
                                  alignment.
   -setcase            float      Sets the threshold for the scores of the
                                  positive matches above which the consensus
                                  is in upper-case and below which the
                                  consensus is in lower-case. By default this
                                  is set to be half of the (weight-adjusted)
                                  number of sequences in the alignment.
   -identity           float      Provides the facility of setting the
                                  required number of identities at a position
                                  for it to give a consensus. Therefore, if
                                  this is set to 100% only columns of
                                  identities contribute to the consensus.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -odirectory2         string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) The sequence alignment to be displayed. Readable set of
   sequences Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.showalign
   Additional (Optional) qualifiers Allowed values Default
   -matrix This is the scoring matrix file used when comparing sequences.
   By default it is the file 'EBLOSUM62' (for proteins) or the file
   'EDNAFULL' (for nucleic sequences). These files are found in the
   'data' directory of the EMBOSS installation. Comparison matrix file in
   EMBOSS data path EBLOSUM62 for protein
   EDNAFULL for DNA
   -refseq If you give the number in the alignment or the name of a
   sequence, it will be taken to be the reference sequence. The reference
   sequence is always show in full and is the one against which all the
   other sequences are compared. If this is set to 0 then the consensus
   sequence will be used as the reference sequence. By default the
   consensus sequence is used as the reference sequence. Any string is
   accepted 0
   -[no]bottom If this is true then the reference sequence is displayed
   at the bottom of the alignment as well as at the top. Boolean value
   Yes/No Yes
   -show What to show
   A (All of the sequences)
   I (Identities between the sequences)
   N (Non-identities between the sequences)
   S (Similarities between the sequences)
   D (Dissimilarities between the sequences)
   N
   -order Output order of the sequences
   I (Input order - no change)
   A (Alphabetical order of the names)
   S (Similarity to the reference sequence)
   I
   -[no]similarcase If this is set True, then when -show is set to
   'Similarities' or 'Non-identities' and a residue is similar but not
   identical to the reference sequence residue, it will be changed to
   lower-case. If -show is set to 'All' then non-identical, non-similar
   residues will be changed to lower-case. If this is False then no
   change to the case of the residues is made on the basis of their
   similarity to the reference sequence. Boolean value Yes/No Yes
   -[no]consensus If this is true then the consensus line is displayed.
   Boolean value Yes/No Yes
   Advanced (Unprompted) qualifiers Allowed values Default
   -uppercase Regions to put in uppercase. If this is left blank, then
   the sequence case is left alone. A set of regions is specified by a
   set of pairs of positions. The positions are integers. They are
   separated by any non-digit, non-alpha character. Examples of region
   specifications are: 24-45, 56-78 1:45, 67=99;765..888
   1,5,8,10,23,45,57,99 Sequence range If this is left blank, then the
   sequence case is left alone.
   -[no]number If this option is true then a line giving the positions in
   the alignment is displayed every 10 characters above the alignment.
   Boolean value Yes/No Yes
   -[no]ruler If this option is true then a ruler line marking every 5th
   and 10th character in the alignment is displayed. Boolean value Yes/No
   Yes
   -width Width of sequence to display Integer 1 or more 60
   -margin This sets the length of the left-hand margin for sequence
   names. If the margin is set at 0 then no margin and no names are
   displayed. If the margin is set to a value that is less than the
   length of a sequence name then the sequence name is displayed
   truncated to the length of the margin. If the margin is set to -1 then
   the minimum margin width that will allow all the sequence names to be
   displayed in full plus a space at the end of the name will
   automatically be selected. Integer -1 or more -1
   -html Use HTML formatting Boolean value Yes/No No
   -highlight Regions to colour if formatting for HTML. If this is left
   blank, then the sequence is left alone. A set of regions is specified
   by a set of pairs of positions. The positions are integers. They are
   followed by any valid HTML font colour. Examples of region
   specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A
   file of ranges to colour (one range per line) can be specified as
   '@filename'. Sequence range full sequence
   -plurality Set a cut-off for the % of positive scoring matches below
   which there is no consensus. The default plurality is taken as 50% of
   the total weight of all the sequences in the alignment. Number from
   0.000 to 100.000 50.0
   -setcase Sets the threshold for the scores of the positive matches
   above which the consensus is in upper-case and below which the
   consensus is in lower-case. By default this is set to be half of the
   (weight-adjusted) number of sequences in the alignment. Any numeric
   value @( $(sequence.totweight) / 2)
   -identity Provides the facility of setting the required number of
   identities at a position for it to give a consensus. Therefore, if
   this is set to 100% only columns of identities contribute to the
   consensus. Number from 0.000 to 100.000 0.0

Input file format

   showalign reads in a set of aligned protein or nucleic sequences.

  Input files for usage example

  File: globins.msf

!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.14
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.15
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.15
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.19
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 0.23
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.21
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.10

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~

   You can specifiy a file of ranges to display in uppercase by giving
   the '-uppercase' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-upper @myfile').

   The format of the range file is:

     * Comment lines start with '#' in the first column.
     * Comment lines and blank lines are ignored.
     * The line may start with white-space.
     * There are two positive (integer) numbers per line separated by one
       or more space or
     * TAB characters.
     * The second number must be greater or equal to the first number.
     * There can be optional text after the two numbers to annotate the
       line.
     * White-space before or after the text is removed.

   An example range file is:


# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

   You can specifiy a file of ranges to highlight in a different colour
   when outputting in HTML format (using the '-html' qualifier) by giving
   the '-highlight' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-highlight @myfile').

   The format of this file is very similar to the format of the above
   uppercase range file, except that the text after the start and end
   positions is used as the HTML colour name. This colour name is used
   'as is' when specifying the colour in HTML in a '' construct, (where
   'xxx' is the name of the colour).

   The standard names of HTML font colours are given in:
   http://http://www.w3.org/TR/REC-html40/types.html and
   http://www.ausmall.com.au/freegraf/ncolour2.htm and
   http://mindprod.com/htmlcolours.html (amongst other places).

   An example highlight range file is:


# this is my set of ranges
12   23         red
 4   5          darkturquoise
67   10348      #FFE4E1

Output file format

   showalign writes out a text file, optionally formatted for HTML.

  Output files for usage example

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------VHLTPE.K.AVTALWG.VN-VD.V.GEA.GR-LLVvY.WTQR..ES.GD.ST
HBB_HORSE  --------VQLSGE.KaAVLALWD.VN-EE.V.GEA.GR-LLVvY.WTQR..DS.GD.SN
HBA_HUMAN  --------------VL.PADKTNV.AA-WGkV.AHAGEYGAEAlERMFLS.PTTKTYFPH
HBA_HORSE  --------------VL.AADKTNV.AA-WSkV.GHAGEYGAEAlERMFLG.PTTKTYFPH
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAD-VAGH.QDI.IR-LFKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAPLSAA.KtKIRSAWAPVYSTY.TSGVDiLVKFFTST.AAQE..PK.KG.TT
LGB2_LUPLU --------GALTESqAaLVKSSWEeFNANIPKHTHRFFILVLE.A.AAKDL.SFLKGTSE
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  PDAVMGnPK..A......G.FSDGlAH..n.KGTF.T..e..CD..H--.DPE..r..GN
HBB_HORSE  PGAVMGnPK..A......HsFGEG.HH..n.KGTF.A..e..CD..H--.DPE..r..GN
HBA_HUMAN  FDLSHG.AQ..G.....AD..TNA.AHv..mPNALsA.....AH...--.DPV.....SH
HBA_HORSE  FDLSHG.AQ..A.....GD..TLA.GH....PGALsN.....AH...--.DPV.....SH
MYG_PHYCA  EAEMKA.EDl.K..VT..T..GAIlKKKGHHEAELKP.aQS.AT.Hk--iPIKYLeFiSE
GLB5_PETMA ADQLKK.AD.rW.AeriiN.vNDA.ASm..TEKMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELQAHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GSVHvSKG.ADAh.PvvKE
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  V.vC..AHHFGKe..PP.Q.aYQ.VvAG..NA.AH..H------
HBB_HORSE  V.vV..ARHFGK...PElQ..YQ.VvAG..NA.AH..H------
HBA_HUMAN  C..VT.AAHLPAe..PA.H..LD.F.AS.sTV.TS..R------
HBA_HORSE  C..ST.AVHLPN...PA.H..LD.F.SS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPG..GADAQGaMN.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGFEKLM.MICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsEElNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 2

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------VHLTPE.K.AVTALWG.VN-VD.V.GEA.GR-LLVvY.WTQR..ES.GD.ST
HBB_HORSE  --------VQLSGE.KaAVLALWD.VN-EE.V.GEA.GR-LLVvY.WTQR..DS.GD.SN
HBA_HORSE  --------------VL.AADKTNV.AA-WSkV.GHAGEYGAEAlERMFLG.PTTKTYFPH
HBA_HUMAN  --------------VL.PADKTNV.AA-WGkV.AHAGEYGAEAlERMFLS.PTTKTYFPH
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAD-VAGH.QDI.IR-LFKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAPLSAA.KtKIRSAWAPVYSTY.TSGVDiLVKFFTST.AAQE..PK.KG.TT
LGB2_LUPLU --------GALTESqAaLVKSSWEeFNANIPKHTHRFFILVLE.A.AAKDL.SFLKGTSE
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  PDAVMGnPK..A......G.FSDGlAH..n.KGTF.T..e..CD..H--.DPE..r..GN
HBB_HORSE  PGAVMGnPK..A......HsFGEG.HH..n.KGTF.A..e..CD..H--.DPE..r..GN
HBA_HORSE  FDLSHG.AQ..A.....GD..TLA.GH....PGALsN.....AH...--.DPV.....SH
HBA_HUMAN  FDLSHG.AQ..G.....AD..TNA.AHv..mPNALsA.....AH...--.DPV.....SH
MYG_PHYCA  EAEMKA.EDl.K..VT..T..GAIlKKKGHHEAELKP.aQS.AT.Hk--iPIKYLeFiSE
GLB5_PETMA ADQLKK.AD.rW.AeriiN.vNDA.ASm..TEKMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELQAHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GSVHvSKG.ADAh.PvvKE
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  V.vC..AHHFGKe..PP.Q.aYQ.VvAG..NA.AH..H------
HBB_HORSE  V.vV..ARHFGK...PElQ..YQ.VvAG..NA.AH..H------
HBA_HORSE  C..ST.AVHLPN...PA.H..LD.F.SS.sTV.TS..R------
HBA_HUMAN  C..VT.AAHLPAe..PA.H..LD.F.AS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPG..GADAQGaMN.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGFEKLM.MICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsEElNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 3

  File: globins.showalign

<pre>
                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxx<font color=green>xxxxxxxxxx</font>xExSxxxxxxxKxxxxxExGxxxLxxxxx<
font color=red>x</font>IxPxxxx<font color=blue>FFxxFx</font>xLxx
HBB_HUMAN  ---<font color=green>-----VHLTP</font>E.K.AVTALWG.VN-VD.V.GEA.GR-LL<
font color=red>V</font>vY.WTQR<font color=blue>..ES.G</font>D.ST
HBB_HORSE  ---<font color=green>-----VQLSG</font>E.KaAVLALWD.VN-EE.V.GEA.GR-LL<
font color=red>V</font>vY.WTQR<font color=blue>..DS.G</font>D.SN
HBA_HUMAN  ---<font color=green>----------</font>-VL.PADKTNV.AA-WGkV.AHAGEYGAE<
font color=red>A</font>lERMFLS<font color=blue>.PTTKT</font>YFPH
HBA_HORSE  ---<font color=green>----------</font>-VL.AADKTNV.AA-WSkV.GHAGEYGAE<
font color=red>A</font>lERMFLG<font color=blue>.PTTKT</font>YFPH
MYG_PHYCA  ---<font color=green>----VLSEGE</font>WqLVLHVWAKVeAD-VAGH.QDI.IR-LF<
font color=red>K</font>SH.ETLE<font color=blue>K.DR.K</font>H.KT
GLB5_PETMA PIV<font color=green>DTGSVAPLSA</font>A.KtKIRSAWAPVYSTY.TSGVDiLVKFF<
font color=red>T</font>ST.AAQE<font color=blue>..PK.K</font>G.TT
LGB2_LUPLU ---<font color=green>-----GALTE</font>SqAaLVKSSWEeFNANIPKHTHRFFILVL<
font color=red>E</font>.A.AAKD<font color=blue>L.SFLK</font>GTSE
Consensus  xxx<font color=green>xxxxxxxxxx</font>xExSxxxxxxxKxxxxxExGxxxLxxxxx<
font color=red>x</font>IxPxxxx<font color=blue>FFxxFx</font>xLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  PDAVMGnPK..A......G.FSDGlAH..n.KGTF.T..e..CD..H--.DPE..r..GN
HBB_HORSE  PGAVMGnPK..A......HsFGEG.HH..n.KGTF.A..e..CD..H--.DPE..r..GN
HBA_HUMAN  FDLSHG.AQ..G.....AD..TNA.AHv..mPNALsA.....AH...--.DPV.....SH
HBA_HORSE  FDLSHG.AQ..A.....GD..TLA.GH....PGALsN.....AH...--.DPV.....SH
MYG_PHYCA  EAEMKA.EDl.K..VT..T..GAIlKKKGHHEAELKP.aQS.AT.Hk--iPIKYLeFiSE
GLB5_PETMA ADQLKK.AD.rW.AeriiN.vNDA.ASm..TEKMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELQAHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GSVHvSKG.ADAh.PvvKE
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  V.vC..AHHFGKe..PP.Q.aYQ.VvAG..NA.AH..H------
HBB_HORSE  V.vV..ARHFGK...PElQ..YQ.VvAG..NA.AH..H------
HBA_HUMAN  C..VT.AAHLPAe..PA.H..LD.F.AS.sTV.TS..R------
HBA_HORSE  C..ST.AVHLPN...PA.H..LD.F.SS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPG..GADAQGaMN.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGFEKLM.MICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsEElNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

</pre>

  Output files for usage example 4

  File: globins.showalign

HBB_HUMAN  HLTPEEKSAVTALWGKVN-VD
HBB_HORSE  Q.sG...a..L...D...-Ee
HBA_HUMAN  -----VL.PADKTNV.AA-WG
HBA_HORSE  -----VL..ADKTNV.AA-WS
MYG_PHYCA  SEGEWqLVLHVWAKVeAd-.A
GLB5_PETMA P.sAA..tKiRsA.AP.YSTY
LGB2_LUPLU A..ESqAaL.KsS.EeF.ANI

  Output files for usage example 6

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------vhltpeEkSavtalwgKvn-vdEvGgeaLgr-llvVyPwtqrFFesFgdLst
HBB_HORSE  --------vqlsgeEkAavlalwdKvn-eeEvGgeaLgr-llvVyPwtqrFFdsFgdLsn
HBA_HUMAN  --------------vlSpadktnvKaa-wgKvGahageygaeaLermflsFpttktyfph
HBA_HORSE  --------------vlSaadktnvKaa-wsKvGghageygaeaLermflgFpttktyfph
MYG_PHYCA  -------vlsegewQlvlhvwakvEad-vaghGqdiLir-lfkshPetlekFdrFkhLkt
GLB5_PETMA pivdtgsvaplsaaEkTkirsawapvystyEtsgvdIlvkfftstPaaqeFFpkFkgLtt
LGB2_LUPLU --------galtesQaAlvkssweEfnanipkhthrffilvleIaPaakdlFsflkgtse
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  pdavmgNpkVKaHGKKVLgAfsdgLahLDNLkgtfAtLSELHcdKLh--VdpeNFRLLgn
HBB_HORSE  pgavmgNpkVKaHGKKVLhSfgegVhhLDNLkgtfAaLSELHcdKLh--VdpeNFRLLgn
HBA_HUMAN  fdlshgSaqVKgHGKKVadALtnaVahVDDMpnalSaLSDLHahKLR--VdpvNFKLLsh
HBA_HORSE  fdlshgSaqVKaHGKKVgdALtlaVghLDDLpgalSnLSDLHahKLR--VdpvNFKLLsh
MYG_PHYCA  eaemkaSedLKkHGvtVLtALgaiLkkkghheaelkpLAqsHatKhK--IpikylEfIse
GLB5_PETMA adqlkkSadVRwHaERIInAVndaVasMDDtekmsmkLrDLsgkhaK--sfqvDpQyfkv
LGB2_LUPLU vpqnnpelqahagkvfkLvyeaaiqlqVtgVvvtdAtLkNLgsvhVskgVadaHFpVVke
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  vLVcVLahhfgkEFTppVqAAyqKvVagVAnaLahKYh------
HBB_HORSE  vLVvVLarhfgkDFTpeLqASyqKvVagVAnaLahKYh------
HBA_HUMAN  cLLvtLaahlpaEFTpaVhASldKfLasVStvLtsKYr------
HBA_HORSE  cLLstLavhlpnDFTpaVhASldKfLssVStvLtsKYr------
MYG_PHYCA  aIIhVLhsrhpgDFgadaqgAmnKaLelfrkdIaaKYkelgyqg
GLB5_PETMA laavIadtvaagDagfeklmSmiciLlrsAy-------------
LGB2_LUPLU aILktIkevvgakWSeeLnSAwtiaydeLAivIkkEmndaa---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 7

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------......E.S.......K..-..E.G...L..-.....P....FF..F..L..
HBB_HORSE  --------......E.........K..-..E.G...L..-.....P....FF..F..L..
HBA_HUMAN  --------------..S.......K..-....G.................F.........
HBA_HORSE  --------------..S.......K..-....G.................F.........
MYG_PHYCA  -------....................-....G...L..-.....P.....F..F..L..
GLB5_PETMA ..............E...............E..............P....FF..F..L..
LGB2_LUPLU --------...................................I.P.....F........
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  .........VK.HGKKVL.A.......LD.L....A.LS.LH..KL.--V...NF.LL..
HBB_HORSE  .........VK.HGKKVL......V..LD.L....A.LS.LH..KL.--V...NF.LL..
HBA_HUMAN  ......S..VK.HGKKV..AL...V...DD.......LSDLH..KLR--V...NFKLL..
HBA_HORSE  ......S..VK.HGKKV..AL...V..LDDL......LSDLH..KLR--V...NFKLL..
MYG_PHYCA  ......S...K.HG..VL.AL................L...H..K..--...........
GLB5_PETMA ......S..V..H......A....V...DD.......L.DL......--...........
LGB2_LUPLU .................L.................A.L..L........V....F.....
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  .L..VL.......FT..V.A...K....VA..L..KY.------
HBB_HORSE  .L..VL......DFT....AS..K....VA..L..KY.------
HBA_HUMAN  .LL..L.......FT..V.AS..K.L..V...L..KY.------
HBA_HORSE  .LL..L......DFT..V.AS..K.L..V...L..KY.------
MYG_PHYCA  ....VL......DF.........K.L.........KY.......
GLB5_PETMA ............D.......S....L...A.-------------
LGB2_LUPLU ..L..........................A...........---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 8

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------......E.S.......K..-..E.G...L..-...v.P....FF..F..L..
HBB_HORSE  --------......E.a.......K..-..E.G...L..-...v.P....FF..F..L..
HBA_HUMAN  --------------..S.......K..-..k.G..........l......F.........
HBA_HORSE  --------------..S.......K..-..k.G..........l......F.........
MYG_PHYCA  -------.......q.........e..-....G...L..-.....P.....F..F..L..
GLB5_PETMA ..............E.t.............E.....i........P....FF..F..L..
LGB2_LUPLU --------......q.a.......e..................I.P.....F........
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  ......n..VK.HGKKVL.A....l..LDnL....A.LSeLH..KL.--V...NFrLL..
HBB_HORSE  ......n..VK.HGKKVL.s....V..LDnL....A.LSeLH..KL.--V...NFrLL..
HBA_HUMAN  ......S..VK.HGKKV..AL...V..vDDm....s.LSDLH..KLR--V...NFKLL..
HBA_HORSE  ......S..VK.HGKKV..AL...V..LDDL....s.LSDLH..KLR--V...NFKLL..
MYG_PHYCA  ......S..lK.HG..VL.AL...l............La..H..K.k--i.....e.i..
GLB5_PETMA ......S..Vr.H.erii.Av...V..mDD.......L.DL.....k--....d.q....
LGB2_LUPLU .................L.........v..v....A.L.nL....v...V...hF.vv..
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  .Lv.VL......eFT..V.Aa..K.v..VA..L..KY.------
HBB_HORSE  .Lv.VL......DFT..l.AS..K.v..VA..L..KY.------
HBA_HUMAN  .LL..L......eFT..V.AS..K.L..Vs..L..KY.------
HBA_HORSE  .LL..L......DFT..V.AS..K.L..Vs..L..KY.------
MYG_PHYCA  .ii.VL......DF......a..K.L......i..KY.......
GLB5_PETMA ....i.......D.......S....L...A.-------------
LGB2_LUPLU .iL..i.......ws..l.sa.......lA..i..e.....---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 9

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
HBB_HUMAN  --------VHLTPE.K.AVTALWG.VN-VD.V.GEA.GR-LLV.Y.WTQR..ES.GD.ST
HBB_HORSE  --------VQLSGE.K.AVLALWD.VN-EE.V.GEA.GR-LLV.Y.WTQR..DS.GD.SN
HBA_HUMAN  --------------VL.PADKTNV.AA-WG.V.AHAGEYGAEA.ERMFLS.PTTKTYFPH
HBA_HORSE  --------------VL.AADKTNV.AA-WS.V.GHAGEYGAEA.ERMFLG.PTTKTYFPH
MYG_PHYCA  -------VLSEGEW.LVLHVWAKV.AD-VAGH.QDI.IR-LFKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAPLSAA.K.KIRSAWAPVYSTY.TSGVD.LVKFFTST.AAQE..PK.KG.TT
LGB2_LUPLU --------GALTES.A.LVKSSWE.FNANIPKHTHRFFILVLE.A.AAKDL.SFLKGTSE
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
HBB_HUMAN  PDAVMG.PK..A......G.FSDG.AH....KGTF.T.....CD..H--.DPE.....GN
HBB_HORSE  PGAVMG.PK..A......H.FGEG.HH....KGTF.A.....CD..H--.DPE.....GN
HBA_HUMAN  FDLSHG.AQ..G.....AD..TNA.AH....PNAL.A.....AH...--.DPV.....SH
HBA_HORSE  FDLSHG.AQ..A.....GD..TLA.GH....PGAL.N.....AH...--.DPV.....SH
MYG_PHYCA  EAEMKA.ED..K..VT..T..GAI.KKKGHHEAELKP..QS.AT.H.--.PIKYL.F.SE
GLB5_PETMA ADQLKK.AD..W.A....N..NDA.AS...TEKMSMK.R..SGKHA.--SFQV.P.YFKV
LGB2_LUPLU VPQNNPELQAHAGKVFK.VYEAAIQLQ.TG.VVTD.T.K..GSVH.SKG.ADA..P..KE
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
HBB_HUMAN  V..C..AHHFGK...PP.Q..YQ.V.AG..NA.AH..H------
HBB_HORSE  V..V..ARHFGK...PE.Q..YQ.V.AG..NA.AH..H------
HBA_HUMAN  C..VT.AAHLPA...PA.H..LD.F.AS..TV.TS..R------
HBA_HORSE  C..ST.AVHLPN...PA.H..LD.F.SS..TV.TS..R------
MYG_PHYCA  A..H..HSRHPG..GADAQG.MN.A.ELFRKD.AA..KELGYQG
GLB5_PETMA LAAV.ADTVAAG.AGFEKLM.MICI.LRS.Y-------------
LGB2_LUPLU A..KT.KEVVGAK..EE.N..WTIAYDE..IV.KK.MNDAA---
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 10

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLST
HBB_HORSE  --------.Q.sG...a..L...D...-Ee.........-............d......N
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PTtKTYFPH
HBA_HORSE  --------------VL..ADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PTtKTYFPH
MYG_PHYCA  -------VlSEGEWqLVLHVWAKVeAd-.AGH.QdI.I.-.FKSh.E.LEK.dR.KH.K.
GLB5_PETMA PIVDTGSVAP.sAA..tKiRsA.AP.YSTY.TS.VDiLVKFFTST.AA.E..PK.KG.t.
LGB2_LUPLU --------GA..ESqAaL.KsS.EeF.ANIPKHTHRFFILv.EiA.AAkDL.SFLKGT.E
HBB_HUMAN  --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLST
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGN
HBB_HORSE  .G................Hs.Ge.vH..........A..........--...........
HBA_HUMAN  F.LSH.sAq..G.....AD.LtnAv..v.dmPNALsA..d..AH..R--...V..k..Sh
HBA_HORSE  F.LSH.sAq........GD.LtLAvG...d.P.ALsN..d..AH..R--...V..k..Sh
MYG_PHYCA  EAEmKAsEDl.K..VT..T.LGAI.KKKGhHeAELKP.aqS.AT.HK--iPIkYLEFiSE
GLB5_PETMA A.QlKKsAD.rW.AeriiN.Vn.Av.Sm.dTeKMSMK.Rd.SGKHAK--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELqAH.GKVFK.VYEaAIQLQvTGvVV.D...KN.GSVHvSKG.ADAh.PvvKE
HBB_HUMAN  PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGN
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
HBB_HORSE  ...V...R....d...El..s.................------
HBA_HUMAN  C.lVT..A.LPA....A.H.sLD.Fl.S.sTV.TS..R------
HBA_HORSE  C.lST..V.LPNd...A.H.sLD.FlsS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPGd.GADA.G.MN.AlELFRKDi.A..KELGYQG
GLB5_PETMA lAAViADTVAAGdAGFEKLMsMICilLRS.Y-------------
LGB2_LUPLU AilKTiKEVV.AkwsEElNs.wTIAYDEl.IViKKeMnDAA---
HBB_HUMAN  VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

  Output files for usage example 11

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlst
HBB_HORSE  --------.Q.SG...a..l...d...-ee.........-............d......n
HBA_HUMAN  --------------Vl.padktnv.aa-wgk..ah.geygaealermfls.pttktyfph
HBA_HORSE  --------------Vl..adktnv.aa-wsk...h.geygaealermflg.pttktyfph
MYG_PHYCA  -------vLSEGEWQlvlhvwakvead-.agh.qdi.i.-.fksh.e.lek.dr.kh.k.
GLB5_PETMA pivdtgsvAP.SAA..tkirsa.ap.ysty.ts.vdilvkfftst.aa.e..pk.kg.t.
LGB2_LUPLU --------GA..ESQaal.kss.eef.anipkhthrffilv.eia.aakdl.sflkgt.e
HBB_HUMAN  --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlst

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgn
HBB_HORSE  .g................hs.ge.vh..........a..........--...........
HBA_HUMAN  f.lsh.saq..g.....ad.ltnav..v.dmpnalsa..d..ah..r--...v..k..sh
HBA_HORSE  f.lsh.saq........gd.ltlavg...d.p.alsn..d..ah..r--...v..k..sh
MYG_PHYCA  eaemkasedl.k..vt..t.lgai.kkkghheaelkp.aqs.at.hk--ipikylefise
GLB5_PETMA a.qlkksad.rw.aeriin.vn.av.sm.dtekmsmk.rd.sgkhak--sfqvdpqyfkv
LGB2_LUPLU vpqnnpelqah.gkvfk.vyeaaiqlqvtgvvv.d...kn.gsvhvskg.adah.pvvke
HBB_HUMAN  pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgn

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------
HBB_HORSE  ...v...r....d...el..s.................------
HBA_HUMAN  c.lvt..a.lpa....a.h.sld.fl.s.stv.ts..r------
HBA_HORSE  c.lst..v.lpnd...a.h.sld.flss.stv.ts..r------
MYG_PHYCA  aiih..hsrhpgd.gada.g.mn.alelfrkdi.a..kelgyqg
GLB5_PETMA laaviadtvaagdagfeklmsmicillrs.y-------------
LGB2_LUPLU ailktikevv.akwseelns.wtiaydel.ivikkemndaa---
HBB_HUMAN  vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------

  Output files for usage example 12

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx
GLB5_PETMA PIVDTGSVAPLSAA.KtKIRSAWAPVYSTY.TSGVDiLVKFFTST.AAQE..PK.KG.TT
HBA_HORSE  --------------VL.AADKTNV.AA-WSkV.GHAGEYGAEAlERMFLG.PTTKTYFPH
HBA_HUMAN  --------------VL.PADKTNV.AA-WGkV.AHAGEYGAEAlERMFLS.PTTKTYFPH
HBB_HORSE  --------VQLSGE.KaAVLALWD.VN-EE.V.GEA.GR-LLVvY.WTQR..DS.GD.SN
HBB_HUMAN  --------VHLTPE.K.AVTALWG.VN-VD.V.GEA.GR-LLVvY.WTQR..ES.GD.ST
LGB2_LUPLU --------GALTESqAaLVKSSWEeFNANIPKHTHRFFILVLE.A.AAKDL.SFLKGTSE
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAD-VAGH.QDI.IR-LFKSH.ETLEK.DR.KH.KT
Consensus  xxxxxxxxxxxxxxExSxxxxxxxKxxxxxExGxxxLxxxxxxIxPxxxxFFxxFxxLxx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx
GLB5_PETMA ADQLKK.AD.rW.AeriiN.vNDA.ASm..TEKMSMK.R..SGKHAk--SFQVdPqYFKV
HBA_HORSE  FDLSHG.AQ..A.....GD..TLA.GH....PGALsN.....AH...--.DPV.....SH
HBA_HUMAN  FDLSHG.AQ..G.....AD..TNA.AHv..mPNALsA.....AH...--.DPV.....SH
HBB_HORSE  PGAVMGnPK..A......HsFGEG.HH..n.KGTF.A..e..CD..H--.DPE..r..GN
HBB_HUMAN  PDAVMGnPK..A......G.FSDGlAH..n.KGTF.T..e..CD..H--.DPE..r..GN
LGB2_LUPLU VPQNNPELQAHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GSVHvSKG.ADAh.PvvKE
MYG_PHYCA  EAEMKA.EDl.K..VT..T..GAIlKKKGHHEAELKP.aQS.AT.Hk--iPIKYLeFiSE
Consensus  xxxxxxSxxVKxHGKKVLxALxxxVxxLDDLxxxxAxLSDLHxxKLRxxVxxxNFKLLxx

                  130       140       150       160       170       180
           ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx
GLB5_PETMA LAAViADTVAAG.AGFEKLM.MICI.LRS.Y-------------
HBA_HORSE  C..ST.AVHLPN...PA.H..LD.F.SS.sTV.TS..R------
HBA_HUMAN  C..VT.AAHLPAe..PA.H..LD.F.AS.sTV.TS..R------
HBB_HORSE  V.vV..ARHFGK...PElQ..YQ.VvAG..NA.AH..H------
HBB_HUMAN  V.vC..AHHFGKe..PP.Q.aYQ.VvAG..NA.AH..H------
LGB2_LUPLU Ai.KTiKEVVGAKwsEElNsaWTIAYDEl.IViKKeMNDAA---
MYG_PHYCA  AiiH..HSRHPG..GADAQGaMN.A.ELFRKDiAA..KELGYQG
Consensus  xLLxVLxxxxxxDFTxxVxASxxKxLxxVAxxLxxKYxxxxxxx

Data files

   showalign reads in scoring matrices to determine the consesnus
   sequence and to determine which matches are similar or not.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.
